ABSTRACT ? Virology Core (Core 2, Leader: Dr. Ann Chahroudi, Emory University) Achieving the proposed Program's goal requires precise quantitation and characterization of SHIV reservoirs and viral dynamics. The Virology Core's objective is to support the Program's two Projects in the rigorous testing of their central hypotheses by providing state-of-the-art virological tools including (i) quantitative PCR analyses of cell-associated SHIV DNA and RNA and plasma SHIV RNA, (ii) combined cell culture and PCR- based assays quantifying the proportion of replication-competent viruses, and (iii) viral sequence analyses by deep sequencing and single genome analysis (SGA). The Virology Core will be led by Dr. Chahroudi, with both routine and novel assays performed in her laboratory at Emory University, and in collaboration with Duke sequencing expertise to provide standardized techniques across Projects 1 & 2 that will permit the ascertainment of interpretable and generalizable results. The Core proposes the following Specific Aims: 1) Quantitative PCR analysis of viral loads in plasma and cells. 2) Estimation of the reservoir size by quantification of replication-competent / inducible virus; and 3) Sequence analyses of pre-ART and rebound viremia in comparison to cell-associated SHIV variants during ART and at rebound. These Aims will make use SIV/SHIV quantification assays developed by Dr. Chahroudi's laboratory and rigorously evaluated for sensitivity, specificity and reproducibility in the animal model to be used, as well as SIV/HIV sequencing expertise of the Duke Human Vaccine Institute. The Virology Core will serve both Projects and interact with both the Administrative and Statistical Core and the Nonhuman Primate Core of this Program to achieve our shared goals. The Virology Core is thus strongly positioned to generate reliable and quantifiable data to rigorously assess the origin, predictors, and virologic correlates of viral rebound in this Program.